Halo: A new beginning
by GeekyLemur0
Summary: "Spartans never die, their just missing in action."- Office of Naval Intelligence Directive 930- just read it
1. Chapter 1

**Hello Fan fiction viewers this is my first fanfic so don't be too harsh in the reviews but if I do something wrong don't hesitate to let me know but remember this is a fan fiction and I plan on making more depending on how this story does, this is a Halo and Fate/Stay Night crossover, this idea has been killing at my head since about a month ago, alright now that thats done R&R**

**P.s. Don't flame, just tell us NICELY what we did wrong ;D**

**We don't own Halo or Fate/Stay Night and if we did…well lets just say i wouldn't be here typing this ;P, instead we would be bathing in water and money instead of fighting those spermy/ herpintitus/ testicular monsters…**

**P.P.s Those spermy/ herpintitus/ testicular monsters are…THE FLOOD**

**P.P.P.s Shirou is still the moron he always was instead of being balls to the walls awesome like Johnson or that one unnamed character you play as in some awesome unknown video game no one ever knew of**

**P.P.P.P.s People die when their killed. If you don't believe mwah look it up **

**P.P.P.P.P.s Leave some fanart of what you think is koolz, i want to see your guyzez artistic abilities.**

Chapter 1: Death of a Hero

It was the year 2553 the war with the covenant was reaching its end with death of the prophet of truth, the leader of the covenant, and with the death of Truth, Chief set out to find Cortana. Chief found Cortana aboard the Covenant capital of High Charity but he also found the Gravemind aboard the ship with her. The Gravemind almost forced Cortana into rampancy but she never gave in as she remembered a certain promise from a certain Spartan. Chief retrieved his A.I. companion and destroyed what remained of High Charity along with the flood was not completely destroyed with the destruction of High Charity and tried to form another Gravemind on the Ark. Chief, the Arbiter, and Sgt. Major Avery Johnson assaulted the control room of the Ark aided by 343 Guilty Spark. When Chief tried to force the destruction of the ring, 343 Guilty Spark killed Sgt. Major Avery Johnson one of Chief's only friends. After the destruction of 343 Guilty Spark, Chief and the Arbiter escaped the Ark onboard the 'Forward Unto Dawn' it was then the portal collapsed causing a slipspace and only the Arbiters half of the ship made it through back to earth while the chiefs half drifted away to the unknown.

_Time Skip 4 years_

The year is 2557. The aft section of the 'Forward Unto Dawn' is drifting through space. Cortana is currently suffering through the final stages of A.I rampancy and is trying to focus so she can keep both Master Chief alive and herself from succumbing to the rampancy while the later part proving to be rather difficult due to how far she is in her rampancy. Cortana had been going on with this trend now for several years now already at the last steps of Rampancy having shown signs of Metastability with Cortana arguing with herself.(1)

"Kill him he doesn't deserve to live."

"NO! Stop it Cortana your better than this."

"He left you to die didn't he?"

"Cortana! Stop thinking like that just calm down."

"But why doesn't he have to suffer like us ?"

"Slowly dying with no hope of survival"

"Cortana desperately tried to process a retort but in the first time in her short existence didn't have an answer to a question".

As Cortana was mulling over the Question and how to respond the rampancy swiftley took over her mind which all in all was quite easy since the rampancy had been battering at her for years now and with almost nothing stopping it now it was almost childs play for it to take over but since Cortana was one of the best, if not the best A.I ever created the rampancy was only slightly able to take over.

She unconsciously began shutting off power to all systems of the ship, including the Cryo-Chamber in which Chief was currently in deep Cryo- Sleep. As the power was being shut down Chiefs vitals began to waver and fade as Cortana shut down the power to the ship while also taking down Chiefs Life Support Systems which in turn choked Chief to death due to lack of Oxygen.

Cortana was abruptly brought back to the present by the lights flickering on and off and the overhead Alarm announcing in a female voice "ALL SYSTEMS DISABLED" when Cortana she looked at the Chiefs pod and saw that the pods Life Support System had been shut off and the Chief was dead.

Cortana slowly floated over to Chief with an disbelieving look on her face and touched the outside of his pod and continued to stare at the pod not moving or talking, not even the nagging voice inside her head was saying anything.

When Cortana finally came to the realization of what she did. She wanted to cry and scream about how this wasn't her fault but her A.I. programming did not have such a code for crying, and on the inside she knew that this was her fault and no one else's. As Cortana was trying to put together what had just happened the nagging voice had finally come back.

" Why so sad? Isn't this what you wanted? Revenge for leaving you to die" the voice said gleefully.

As Cortana thought about what the voice had said she began to cry virtual teams while slowly sliding down Chiefs Cryo-Tube in her grief and sadness, she slowly started to lose control and her rampancy quickly took over and she began to think herself to death as her body started to shift to a reddish color she began to fade away slowly from the bottom to her head, but before Cortana was completely overwhelmed by the rampancy she managed to mutter out a few words from her tear stricken face "Im sorry John". The room was then swallowed in complete darkness and the chief was not to be seen for a long time. —

_John's nightmare-post death_

He woke up not knowing what happened, when he looked around he expected the Cyro-Tube room but what he saw was a blank dusty clearing with nothing around but the bodies of UNSC marines and Covenant that were laying all around him, he took notice of a body that started jolting around on the ground then realized what was happening.

The flood was here and were infecting, he reached for his MA5D assault rifle only to realize it was gone. He checked around him for any weapons he quickly noticed that there were none.

The Spartan grunted as he knew this was going to be a CQC(_Close Quarter Combat_) battle with the flood which often was suicide against so many flood.

There were suddenly overwhelming numbers of flood infection forms that were taking over dead elites as well as marines bodies.

_John _had seen many twisted things in war, marines bodies ripped in half, elites decapitating civilians, and children dead in the streets, but nothing compared to the flood mutilating and transforming dead corpses for the purpose of wiping out all sentient life in the galaxy, or in this case him.

_John _knew the odds of survival were slim to none but he still charged the flood as he was about to kill the first one he noticed his shields were starting to flare up despite not being attacked by any flood yet.

Then all sudden he started to fall through the floor until he was in empty space above a planet then he noticed something…something he hadn't seen in a long time

It was Earth.]"


	2. Chapter 2

**A/N: Hey everyone sorry I didn't update schools back so I can't update week upon week but I'll try to update as soon as possible and thanks for the reviews too! And all the follows even favorites :D Well until next time everyone, enjoy the story :D**

**MANDABLES:Brarg**

As Chief was glancing at earth he noticed how Africa hadn't been 'glassed' he also noticed all of the ODP's(Orbital Defense Platform) that were guarding Earth weren't there either.

While John was comparing this earth to his memory of earth, it slowly dawned on him that he was slowly came to the realization that he was falling rapidly towards earth particularly in the direction of Japan.

_Rin Tohsaka_

Rin Tohsaka was currently chanting the incantation to summon her hero so that she could participate in the 5th Holy Grail War while in her head she was mentally preparing for whatever hero would come through the summoning circle, she hoped it was from the saber class, which if the servant was could guarantee her the victory she hoped for, but she wasn't prepared for who her Hero was though…

She suddenly felt the room rumble as the summoning circle started to brighten, immediately the room was bathed in a blinding flash of red. Rin felt a sense of awe at seeing a hero being summoned, but with a dull glow the summoning circle dimmed out, then disappeared almost as if nothing was there.

She looked at the area where the summoning circle had once been but it had completely disappeared she started to feel a knot grow in her stomach at the thought of failure before she had a chance to win the war. Rin shakily got up as she looked over at the area in which the summoning circle disappeared.

She thought with a nod "Maybe I just said the words wrong? Ill try the summoning again at another time when I have more crysta….

Rin was cut off when the room started to rumble violently and the summoning circle reappeared again while shining brighter than ever before, while looking like similarly like an exploding lightbulb She quickly gathered herself and evaluated the situation, she could still feel the rumbling and it was getting closer with every second that passed.

'BOOM!'

Rin covered her from the dust that had gathered in the collapsing of her roof, as the dust settled down her eyes opened and adjusted to the darkness to see what had crashed through her roof. What had come through her ceiling was an olive green armored man with a strange helmet and gold visor, while on the soldiers left breastplate was the numbers 117 clearly labeled in white. but what really interested her was the strange looking rifle on his back which was probably his noble phantasm Rin watched as the armored man stood up from his crouched position towering over her at least 2 feet, she was intimated to say the least, as Rin was analyzing the armored man she glanced at her hand to check if she had the command seals and was a little relived when the red summoning symbols were there.

She asked the armored man "What class are you?" she tried to say it in a stern voice and kept her stance of that a superior officer would say to a Private.

The armored man replied in a deep voice "My class is Archer ma'am." He then saluted her with his both his arms held at his back.

She was stunned at his actions and the armor he was wearing intimidated anyone who was near, while a little annoyed that he called her "ma'am" she wasn't that old.

She told the armored man "I am Rin Tohsaka your master, and don't call me "Ma'am" it makes me feel old."

Master Chief nodded while making sure to later obtain information about his master and the planet itself as all he knew was the information inserted into his head before he plummeted into Earths atmosphere.

_Flashback: 5 minutes before landing_

Chief could see the Earth approaching and once he saw the lack of changes he began questioning a lot of things.

But out of nowhere he had a massive headache, even with his Spartan augmentations it was painful, he was getting flashes of battles and wars and started realizing that he was also getting the information as if he was remembering these things as if they were memories.

After about ten minutes the flashes stopped and he knew all about the Holy Grail Wars and he continued to plummet towards the earth.

_End Flashback _

"_What is your name from legend and class hero"_

"_Master Chief Petty Officer Sierra-117, class Archer Master" Stated Chief_

"_I have never heard of such a name as that and with those armor and weapons it makes him look like a space soldier or something" thought Rin._

"_I…see then" Rin said with a uneasy smile. _

Chief asked "What's our next course of action?"

Rin said "We're off to pay someone a visit but I need you to remain hidden until I call for you."

Chief replied with a neutral tone "is this person an ally or an enemy?"

Rin replied with an equally neutral tone "Ally hopefully, turn into astral form Archer"

Chief gave a swift nod and activated his active camouflage, hiding him from all sight aside from the glimmer of light here and there

Rin was surprised to say the very least, she wondered what the full extent of his abilities were, all she saw was a glint of light every now and then but she knew in the dark he would be invisible to the untrained eye.

_Shirou's House_

Rin was currently talking to Shirou about something important that was for sure, the Spartan could tell by the serious looks on they're faces and with his augmented hearing he could hear Rin was asking Shirou some questions about his magic abilities.

Rin asked Shirou "What kind of magic do you use, all the types you use."

Shirou replied sheepishly while scratching the back of his head "Reinforcement and projection magic…"

Rin sweat dropped at that.

She thought Shirou just might make a good ally to her, but she clearly thought wrong as she was just wasting her time with him.

John was waiting just outside the room with his active camouflage activated he listened to the whole conversation and watched as Rin quickly became annoyed with Shirou but then something suddenly appeared on his motion sensor and disappeared he pulled out his MA5D and aimed it toward the intruders general direction.

He took aim at the intruder and uncloaked before he took another step.

Lancer had not noticed the man walking in due to the Spartans invisibility, while he was walking in but wasn't surprised at this as he expected this because he saw Rin walk in and noticed the command seals on her hand.

Lancer looked at the Spartan and upon further inspection he saw difference between the two. He didn't care but something felt odd about this hero he never seen anything like him before which made him a bit curious to say the least.

Chief stood firm as he aimed at Lancer with his assault rifle. He asked "Who are you? how did you get in?".

Lancer looked unfazed by both of his questions and he replied with a laid-back tone "I am Lancer and you are?"

Chief stood there with his gun still trained on Lancer and said "I don't plan on telling you."

Lancer looked a little annoyed at that because he revealed his servant class so he should too by "You know its common courtesy to introduce yourself to someone who tells you their name."

Chief replied in his usual calm yet stern voice "I wasn't exactly raised to show common courtesy. To anyone." He said the last part in a cold tone even lancer shivered a little bit at that.

Lancer then replied tauntingly "wow…..You must have had a pretty shitty childhood growing up."

Chief tightened his grip on his gun due to the fact that Lancer pretty much insulted Doctor Halsey and his fellow Spartan brothers and sisters.

Lancer grinned knowing he struck a nerve with him "Oh dear it seems I've struck a nerve didn't I? Is it cause I made fun of your mommy?"

CHINK…. the room echoed from the one shot as a thin cut appeared on Lancers face and small amounts of blood began to drip down his face. Lancer knew that if the visor wasn't there he would probably see Chiefs glare right now which could probably kill a lesser man thankfully he was a Legendary hero after also all the glare was able to do was get his blood pumping and adrenaline rushing.

Lancer's grin turned into a gleeful smirk now knowing the fight was about to begin and tightened his muscles ready to leap like a ferocious dog.

Chief realized that Lancer was about to charge at him. He quickly opened fire with his MA5D aiming for Lancers arms to take out most likely his noble phantasm and his spear while shooting chief quickly ran out of ammo and ducked behind a wall to quickly reload while keeping an eye on his radar.

Lancer charged chief intending to hit him with his Gae Bolg seeing as the only times really available to hit The Spartan were when he was reloading or when the Green behemoth was taking cover as lancer charged the wall, lancer heard a faint 'clink' and when he realized the mistake he made it was far too late, due to the Holy Grail War taking place in Japan, a lot of the doors were super thin which would make it incredibly easy for anything to force its way through the wall, and when you have the master chief… well he ends up over doing things….a lot and Lancer due to his E in luck tripped face forward into the Chiefs Titanium-A knee cap which then the Chief Threw Lancer 7 feet through the wood floor, past the concrete, eventually making it to the muddy dirt covering lancer in a brown liquid so intense that Lancer almost started looking like a real dog.

Chief then preceded to open fire on lancers prone form with his Assault Rifle making sure to hit Lancer in the general direction of his vital organs but apparently Lancers armor isn't for show as all the bullets did was dent Lancers armor a lot.

Chief continued to fire his Assault rifle but heard a swift click signifying he needed to reload. Chief's sixth sense went crazy and he only managed to turn around halfway before getting butted with the end of Lancers Gae Bolg.

Lancer took this opportunity to backslap the Chief hard adding a bit more magical force into the punch to make the chief slide 15 or so feet before the Chief ripped out his combat knife and slammed it into the ground to slow his decent.

Chief threw his rifle aside while lazily twirling his combat knife, while getting into the stance he would normally kill elites with now ready for CQC (close quarters combat)

" Oh, going to fight fair now?" Lancer said teasingly, while lightly hopping to loosen his mussels John didn't respond to the remark instead slowly getting more into his stance in which he could intercept a blow from Lancers spear and strike back with his knife almost like that of a cobra while Lancer gripped his spear while thinking on how to attack the Spartan seeing how he was fighting a hardcore war veteran and not some newbie soldier they continued to stare each other down waiting until a opening came and presented itself to them to. A tense silence enveloped the two until a leaf slowly fell down and the two slightly adjusted their forms to prepare to charge and when the leaf fell and hit the floor the world exploded in both sound and light.

GAE BOLG! shouted Lancer while pouring all his Mana into this one attack in an attempt to pierce the Chiefs armor but due to all the genetic modifications and the recent war Chiefs reflexes kicked in and he barely dodges the spear, with the spear slightly skimming the Chiefs armor producing a screeching noise that stunned Lancer due to his sensitive hearing Chiefs breastplate barely missing what would have been a fatal blow.

As the spear skims Chief, Shirou comes running out of the house with the spear flying by and with shirou ducking just in time to not get his head blown off but due to Gae Bolg's special power the spear pierced through Shirou's heart and he collapsed.

_Shirou- 5 minutes prior to wound_

Shirou was sheepishly smiling at Rin seeing her reaction to his statement of only using 2 types of magic while not truly understanding what he said in the eyes of a magus like her, seeing as what he knew probably wasn't even enough to make an apprentice mage.

Rin then felt a sudden feeling of danger through her connection to Archer and she knew her servant had engaged in combat with another servant but she didn't know who it was with and didn't know if she should go help.

She knew she had to do something because Shirou might get killed in the crossfire of the fight between Heroes due to his overwelming need to help everyone he can.

Rin asked Shirou in a demanding yet polite voice "Would you mind going for a walk with me?"

Shirou blushed at the question not knowing her intentions he replied "O-okay why"

Rin quickly got up and headed towards the door while Shirou quickly followed a little excited yet curious on what they might do, and thats when they heard the gunshots.

Shirou was confused but then relized someone could be hurt and rushed outside despite Tohsakas warnings, while quickly ran outside the door he only got a glimpse of what lay before him before a red spear came flying in his direction.

_End Flashback_

Shirou vision started to fade as he fell onto his side on the already dirty floor with more blood leaking everywhere, giving him only a few more minutes to live before he would bleed to death, while on the floor Shirou would occasionally mutter out "Tohsaka" before choking a bit on his blood

Rin was scared by the sudden stabbing and all the blood, but she knew that Shirou needed her help if he wanted to live so she immediately went to take out the spear and help pressure the wound with one hand while pulling out one of her best jewels to help heal him.

Master Chief quickly realized his master was in the presence of an immediate danger and was not completely aware of her surroundings. He quickly sprinted towards Rin to grab her and Shirou, and after he had them at a safe distance he would deal with Lancer.

Rin saw that Chief was sprinting towards her at an extreme speed only barely visable from his after-images.

Lancer also sprinted towards Rin and Shirou to grab his spear to get another attempt at killing ether the Spartan or the vulnerable master.

Shirou was in extreme pain and could hardly notice anything but due to Tohsaka's jewel it healed him slightly while giving him complete numbness in that area, then he felt a breeze and looked up to see him alone with the blue armored man who gave him a predatory look.

Lancer grabbed his spear that was near the side of shirou, he noted that Rin and her servant had disappeared, which ticked off Lancer a bit seeing as how they had a good fight on going, but it had ended because of the boy in front of him and with a gleeful look on his face Lancer looked down at Shirou and rose his spear up to strike him down, for revenge for interrupting his fight of course.

As Shirou was holding his hands up to attempt to block the sword he noticed through his fingers a massive distortion over 8 feet tall behind lancer, then in the blink of an eye a blue blade was impaled through lancer and a massive alien with mandibles wearing sliver ordinate armor appeared from the distortion.

Lancer looked over his shoulder to see a massive 'thing' behind him while he felt the blade come out of him slowly and very painfully burning his internal organs. Lancer fell on the ground coughing up blood. Lancer asked the 'thing' "Who or what are you?"

The Arbiter replied "I am Ripa 'Moramee."

"And I live only to serve as my masters sword"

Ripa 'Moramee turned his attention to the human with the slight wound in the heart that was rapidly healing over. He glanced once to see what he looked like and said "Your race was always a pitiful one, _human and it shall always be." _He then raised his sword to strike down Shirou.

All of the sudden there was a bright flash accompanied by a glowing circle on the floor, while in front of Shirou a woman appeared at the last second and blocked the Arbiter's attack with what seemed like solidified air.

Shirou was confused at what was happening but thankful she had saved him.

Ripa glared at her with killing intent in his eyes. But he knew he wasn't at full strength to fight a servant just yet so he activated his camouflage and pushed the girl away and rapidly dashed away.

Shirou was confused, happy and tired all at the same time. He took one last look at the woman who saved him and fell unconscious, with the last thing he heard was "Are you my master?"

Master Chief and Rin had been watching the whole encounter from a nearby roof top while Chief had been watching through his sniper rifle and had almost fired at the last second if the girl hadn't appeared.

Rin was to say the least surprised that a Saber class appeared in front of Shirou. She felt jealous and a bit relieved at the same time, that he was very lucky to get a powerful saber yet happy that he had lived.

Chief however was unaffected by the matter except for the Arbiter being here as that was his main concern so far.

He thought to himself "What is an Arbiter doing here?" He knew that this wasn't the same Arbiter he knew, this one had a killers intent like no other and his last sentence is what confirmed it for Chief knew the Arbiter wouldn't say things like that especially what the Arbiter had went through for Humanity.

But he knew he would have to deal with him sooner than later, although he would prefer later after coming up with a plan.

Rin had finally decided she had seen enough. She told her servant "Lets, go we'll talk to him another time."

Chief just nodded at this and picked up Rin and blurred away.

Rin had found them a new hotel to stay in since the one she had summoned the Chief in, he crashed through. She thought with a smirk on her face, "It was quite the entrance to say the least."

She then thought to herself as she started to close her eyes "Master Chief Petty Offer Sierra-117…" "he must have come from a military background of some sort". She shrugged it off though as she was now falling asleep.

Chief was still up, despite the fact it was now 2:48 A.M. Japanese time.

Chief was currently recalling all the events that had happened to him over the course of the day he just had.

He understood the Holy Grail wars perfectly and what the participants were striving for but he didn't like how he was ordered around by someone all the time it reminded him of ONI sending him on suicide runs into enemy territory all the time.

The only people he was okay with commanding him around was his 'mother' Dr. Catherine Halsey, his instructor Mendez, Captain Keyes, and…Cortana.

He grimaced at the thought of losing Cortana, he and the A.I. had been through a lot together. He didn't remember how he died but he knew that he had left Cortana behind.

He knew the Holy Grail granted whatever you desired most in this world but he didn't know what he wanted most in his life.


End file.
